mvpart {mvpart} | R Documentation |
Wrapper function for fitting and plotting rpart
models
mvpart(form, data, minauto = TRUE, size, xv = c("1se", "min", "pick", "none"), xval = 10, xvmult = 0, xvse = 1, snip = FALSE, plot.add = TRUE, text.add = TRUE, digits = 3, margin = 0, uniform = FALSE, which = 4, pretty = TRUE, use.n = TRUE, all.leaves = FALSE, bars = TRUE, legend, bord = FALSE, xadj = 1, yadj = 1, prn = FALSE, branch = 1, rsq = FALSE, big.pts = FALSE, pca = FALSE, interact.pca = FALSE, wgt.ave.pca = FALSE, keep.y = TRUE, ...)
form |
As for rpart function.
Arguments to rpart can be passed by ....
|
data |
Optional data frame in which to interpret the variables named in the formula |
minauto |
If TRUE uses smart minsplit and minbucket based on N cases.
|
size |
The size of tree to be generated. |
xv |
Selection of tree by cross-validation: "1se" - gives best tree within one SE of the overall best,
"min" - the best tree, "pick" - pick the tree size interactively,
"none" - no cross-validation.
|
xval |
Number of cross-validations or vector defining cross-validation groups. |
xvmult |
Number of multiple cross-validations. |
xvse |
Multiplier for the number of SEs used for xv = "1se" .
|
plot.add |
Plot the tree and (optionally) add text. |
text.add |
Add output of text.rpart to tree.
|
snip |
Interactively prune the tree. |
digits |
Number of digits on labels. |
margin |
Margin around plot, 0.1 gives an extra 10 percent space around the plot. |
uniform |
Uniform lengths to the branches of the tree. |
which |
Which split labels and where to plot them, 1=centered, 2 = left, 3 = right and 4 = both. |
pretty |
Pretty labels or full labels. |
use.n |
Add number of cases at each node. |
all.leaves |
Annotate all nodes. |
bars |
If TRUE adds barplots to nodes.
|
legend |
If TRUE adds legend for mrt and classification trees.
|
bord |
Border (box) around the barplots. |
xadj, yadj |
Adjust the size of the individual barplots (default = 1). |
prn |
If TRUE prints tree details.
|
branch |
Controls spread of branches: 1=vertical lines, 0=maximum slope. |
rsq |
If TRUE gives "rsq" plot.
|
big.pts |
Plot colored points at leaves – useful to link to PCA plot. |
pca |
If TRUE plots PCA of group means and add species and site information.
|
interact.pca |
If TRUE runs interactive PCA. See rpart.pca .
|
wgt.ave.pca |
If TRUE plot weighted averages acorss sites for species.
|
keep.y |
If TRUE y values are returned.
|
... |
... other arguments passed to rpart .
|
an object of class rpart
, a superset of class tree
.
data(spider) mvpart(data.matrix(spider[,1:12])~herbs+reft+moss+sand+twigs+water,spider) # defaults mvpart(data.matrix(spider[,1:12])~herbs+reft+moss+sand+twigs+water,spider,xv="p") # pick the tree size # pick cv size and do PCA fit <- mvpart(data.matrix(spider[,1:12])~herbs+reft+moss+sand+twigs+water,spider,xv="1se",pca=TRUE) rpart.pca(fit,interact=TRUE,wgt.ave=TRUE) # interactive PCA plot of saved multivariate tree